HEADER LIGASE 31-JUL-17 5Y3T TITLE CRYSTAL STRUCTURE OF HETERO-TRIMERIC CORE OF LUBAC: HOIP DOUBLE-UBA TITLE 2 COMPLEXED WITH HOIL-1L UBL AND SHARPIN UBL COMPND MOL_ID: 1; COMPND 2 MOLECULE: RANBP-TYPE AND C3HC4-TYPE ZINC FINGER-CONTAINING PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 1-140; COMPND 5 SYNONYM: HEME-OXIDIZED IRP2 UBIQUITIN LIGASE 1 HOMOLOG,HOIL-1,RING- COMPND 6 TYPE E3 UBIQUITIN TRANSFERASE HOIL-1,UBCM4-INTERACTING PROTEIN 28, COMPND 7 UBIQUITIN-CONJUGATING ENZYME 7-INTERACTING PROTEIN 3; COMPND 8 EC: 2.3.2.27; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE RNF31; COMPND 12 CHAIN: B; COMPND 13 FRAGMENT: UNP RESIDUES 474-630; COMPND 14 SYNONYM: HOIL-1-INTERACTING PROTEIN,HOIP,PUTATIVE ARIADNE-LIKE COMPND 15 UBIQUITIN LIGASE,PAUL,RING FINGER PROTEIN 31,RING-TYPE E3 UBIQUITIN COMPND 16 TRANSFERASE RNF31; COMPND 17 EC: 2.3.2.27; COMPND 18 ENGINEERED: YES; COMPND 19 MOL_ID: 3; COMPND 20 MOLECULE: SHARPIN; COMPND 21 CHAIN: C; COMPND 22 FRAGMENT: UNP RESIDUES 163-341; COMPND 23 SYNONYM: SHANK-ASSOCIATED RH DOMAIN-INTERACTING PROTEIN,SHANK- COMPND 24 INTERACTING PROTEIN-LIKE 1,MSIPL1; COMPND 25 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: RBCK1, RBCK, UBCE7IP3, UIP28; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 11 ORGANISM_COMMON: MOUSE; SOURCE 12 ORGANISM_TAXID: 10090; SOURCE 13 GENE: RNF31, PAUL; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 15 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 16 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 17 MOL_ID: 3; SOURCE 18 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 19 ORGANISM_COMMON: MOUSE; SOURCE 20 ORGANISM_TAXID: 10090; SOURCE 21 GENE: SHARPIN, CPDM, SIPL1; SOURCE 22 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 23 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 24 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS HOIP, HOIL-1L, SHARPIN, LINEAR-UBIQUITIN ASSEMBLY COMPLEX, NF-KB KEYWDS 2 ACTIVATION, LUBAC TETHERING MOTIF, LUBAC STABILIZATION, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR A.TOKUNAGA,H.FUJITA,M.ARIYOSHI,I.OHKI,H.TOCHIO,K.IWAI,M.SHIRAKAWA REVDAT 3 22-NOV-23 5Y3T 1 REMARK REVDAT 2 25-DEC-19 5Y3T 1 JRNL REVDAT 1 02-MAY-18 5Y3T 0 JRNL AUTH H.FUJITA,A.TOKUNAGA,S.SHIMIZU,A.L.WHITING,F.AGUILAR-ALONSO, JRNL AUTH 2 K.TAKAGI,E.WALINDA,Y.SASAKI,T.SHIMOKAWA,T.MIZUSHIMA,I.OHKI, JRNL AUTH 3 M.ARIYOSHI,H.TOCHIO,F.BERNAL,M.SHIRAKAWA,K.IWAI JRNL TITL COOPERATIVE DOMAIN FORMATION BY HOMOLOGOUS MOTIFS IN HOIL-1L JRNL TITL 2 AND SHARPIN PLAYS A CRUCIAL ROLE IN LUBAC STABILIZATION. JRNL REF CELL REP V. 23 1192 2018 JRNL REFN ESSN 2211-1247 JRNL PMID 29694895 JRNL DOI 10.1016/J.CELREP.2018.03.112 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.19 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 17862 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.190 REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.240 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.300 REMARK 3 FREE R VALUE TEST SET COUNT : 1413 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.46 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1219 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.89 REMARK 3 BIN R VALUE (WORKING SET) : 0.2790 REMARK 3 BIN FREE R VALUE SET COUNT : 113 REMARK 3 BIN FREE R VALUE : 0.2970 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3315 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 6 REMARK 3 SOLVENT ATOMS : 21 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 65.22 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.06000 REMARK 3 B22 (A**2) : 0.03000 REMARK 3 B33 (A**2) : -0.09000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.03000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.396 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.256 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.220 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.857 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.964 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.942 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3391 ; 0.014 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3227 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4597 ; 1.703 ; 1.957 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7415 ; 1.004 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 421 ; 7.086 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 161 ;34.712 ;23.789 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 568 ;16.935 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 29 ;16.127 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 505 ; 0.087 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3859 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 782 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1693 ; 4.694 ; 6.153 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1692 ; 4.694 ; 6.151 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2111 ; 6.466 ; 9.224 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2112 ; 6.465 ; 9.225 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1698 ; 5.730 ; 6.822 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1698 ; 5.730 ; 6.821 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2487 ; 8.551 ; 9.966 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3653 ;10.331 ;48.908 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3654 ;10.330 ;48.913 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5Y3T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 31-JUL-17. REMARK 100 THE DEPOSITION ID IS D_1300004614. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-MAR-17 REMARK 200 TEMPERATURE (KELVIN) : 95.0 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-17A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98000 REMARK 200 MONOCHROMATOR : SI(111) CRYSTALS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19275 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : 0.09200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.44 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.5 REMARK 200 DATA REDUNDANCY IN SHELL : 4.20 REMARK 200 R MERGE FOR SHELL (I) : 0.52000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 4DBG REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MAGNESIUM SULFATE, MES, PH 6.5, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 71.95100 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.86600 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 71.95100 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 29.86600 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 9060 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21410 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -61.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 SER A 137 REMARK 465 LEU A 138 REMARK 465 ASN A 139 REMARK 465 PRO A 140 REMARK 465 ASP B 630 REMARK 465 GLY C 155 REMARK 465 PRO C 156 REMARK 465 LEU C 157 REMARK 465 GLY C 158 REMARK 465 SER C 159 REMARK 465 PRO C 160 REMARK 465 GLU C 161 REMARK 465 PHE C 162 REMARK 465 SER C 163 REMARK 465 SER C 164 REMARK 465 GLY C 165 REMARK 465 ASN C 166 REMARK 465 PHE C 167 REMARK 465 LYS C 168 REMARK 465 ARG C 301 REMARK 465 GLU C 302 REMARK 465 VAL C 303 REMARK 465 SER C 304 REMARK 465 GLY C 305 REMARK 465 GLN C 306 REMARK 465 SER C 307 REMARK 465 LEU C 308 REMARK 465 GLN C 309 REMARK 465 ASN C 310 REMARK 465 SER C 311 REMARK 465 LYS C 312 REMARK 465 MET C 313 REMARK 465 ASP C 314 REMARK 465 ARG C 315 REMARK 465 LYS C 316 REMARK 465 LEU C 317 REMARK 465 GLY C 318 REMARK 465 LEU C 319 REMARK 465 PHE C 320 REMARK 465 PRO C 321 REMARK 465 GLN C 322 REMARK 465 SER C 323 REMARK 465 LEU C 324 REMARK 465 GLY C 325 REMARK 465 LEU C 326 REMARK 465 PRO C 327 REMARK 465 HIS C 328 REMARK 465 ASP C 329 REMARK 465 LEU C 330 REMARK 465 GLN C 331 REMARK 465 PRO C 332 REMARK 465 SER C 333 REMARK 465 SER C 334 REMARK 465 SER C 335 REMARK 465 SER C 336 REMARK 465 LEU C 337 REMARK 465 PRO C 338 REMARK 465 SER C 339 REMARK 465 PRO C 340 REMARK 465 SER C 341 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 56 NE - CZ - NH2 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG B 474 NE - CZ - NH2 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG B 570 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 ARG B 570 NE - CZ - NH2 ANGL. DEV. = -4.4 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 GLU A 3 -126.99 -71.99 REMARK 500 LYS A 4 36.30 -98.20 REMARK 500 ARG A 38 53.85 39.45 REMARK 500 PRO A 51 -3.62 -59.90 REMARK 500 MET A 66 -4.07 72.89 REMARK 500 SER A 116 -31.24 -38.53 REMARK 500 ARG A 120 -31.39 -143.65 REMARK 500 THR B 626 108.90 -50.69 REMARK 500 SER C 231 49.44 -75.76 REMARK 500 SER C 233 -122.56 56.14 REMARK 500 SER C 234 80.77 49.59 REMARK 500 SER C 286 -9.45 -157.51 REMARK 500 ALA C 299 70.12 -156.43 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 701 DBREF 5Y3T A 1 140 UNP Q9WUB0 HOIL1_MOUSE 1 140 DBREF 5Y3T B 474 630 UNP Q924T7 RNF31_MOUSE 474 630 DBREF 5Y3T C 163 341 UNP Q91WA6 SHRPN_MOUSE 163 341 SEQADV 5Y3T GLY B 473 UNP Q924T7 EXPRESSION TAG SEQADV 5Y3T GLY C 155 UNP Q91WA6 EXPRESSION TAG SEQADV 5Y3T PRO C 156 UNP Q91WA6 EXPRESSION TAG SEQADV 5Y3T LEU C 157 UNP Q91WA6 EXPRESSION TAG SEQADV 5Y3T GLY C 158 UNP Q91WA6 EXPRESSION TAG SEQADV 5Y3T SER C 159 UNP Q91WA6 EXPRESSION TAG SEQADV 5Y3T PRO C 160 UNP Q91WA6 EXPRESSION TAG SEQADV 5Y3T GLU C 161 UNP Q91WA6 EXPRESSION TAG SEQADV 5Y3T PHE C 162 UNP Q91WA6 EXPRESSION TAG SEQRES 1 A 140 MET ASP GLU LYS THR LYS LYS ALA GLU GLU MET ALA LEU SEQRES 2 A 140 SER LEU ALA ARG ALA VAL ALA GLY GLY ASP GLU GLN ALA SEQRES 3 A 140 ALA ILE LYS TYR ALA THR TRP LEU ALA GLU GLN ARG VAL SEQRES 4 A 140 PRO LEU ARG VAL GLN VAL LYS PRO GLU VAL SER PRO THR SEQRES 5 A 140 GLN ASP ILE ARG LEU CYS VAL SER VAL GLU ASP ALA TYR SEQRES 6 A 140 MET HIS THR VAL THR ILE TRP LEU THR VAL ARG PRO ASP SEQRES 7 A 140 MET THR VAL ALA SER LEU LYS ASP MET VAL PHE LEU ASP SEQRES 8 A 140 TYR GLY PHE PRO PRO SER LEU GLN GLN TRP VAL VAL GLY SEQRES 9 A 140 GLN ARG LEU ALA ARG ASP GLN GLU THR LEU HIS SER HIS SEQRES 10 A 140 GLY ILE ARG ARG ASN GLY ASP GLY ALA TYR LEU TYR LEU SEQRES 11 A 140 LEU SER ALA ARG ASN THR SER LEU ASN PRO SEQRES 1 B 158 GLY ARG GLN ASP LYS MET ARG LYS GLU GLY LEU GLN LEU SEQRES 2 B 158 VAL SER MET ILE GLN GLU GLY GLU THR ALA GLY ALA SER SEQRES 3 B 158 PRO GLU GLU VAL PHE SER ALA LEU GLN TYR SER GLY THR SEQRES 4 B 158 GLU VAL PRO LEU GLN TRP LEU ARG SER GLU LEU SER TYR SEQRES 5 B 158 VAL LEU GLU MET VAL ALA GLU LEU ALA GLY GLN GLN ASP SEQRES 6 B 158 PRO GLU LEU GLY ALA PHE SER CYS GLN GLU ALA ARG LYS SEQRES 7 B 158 ALA TRP LEU ASP ARG HIS GLY ASN LEU ASP GLU ALA VAL SEQRES 8 B 158 GLU GLU CYS VAL ARG ALA ARG ARG ARG LYS VAL HIS GLU SEQRES 9 B 158 LEU GLN SER LEU GLY PHE GLY PRO LYS GLU GLY SER LEU SEQRES 10 B 158 GLN ALA LEU PHE GLN HIS GLY GLY ASP VAL ALA ARG ALA SEQRES 11 B 158 LEU THR GLU LEU GLN ARG GLN ARG LEU GLU PRO PHE HIS SEQRES 12 B 158 GLN ARG LEU TRP ASP ARG ASP PRO GLU PRO THR PRO CYS SEQRES 13 B 158 TRP ASP SEQRES 1 C 187 GLY PRO LEU GLY SER PRO GLU PHE SER SER GLY ASN PHE SEQRES 2 C 187 LYS LYS GLU GLU LEU ALA THR ARG LEU SER GLN ALA ILE SEQRES 3 C 187 ALA GLY GLY ASP GLU LYS ALA ALA ALA GLN VAL ALA ALA SEQRES 4 C 187 VAL LEU ALA GLN HIS HIS VAL ALA LEU ASN VAL GLN LEU SEQRES 5 C 187 MET GLU ALA TRP PHE PRO PRO GLY PRO ILE ARG LEU GLN SEQRES 6 C 187 VAL THR VAL GLU ASP ALA THR SER VAL LEU SER SER SER SEQRES 7 C 187 SER SER ALA HIS VAL SER LEU LYS ILE HIS PRO HIS CYS SEQRES 8 C 187 SER ILE ALA ALA LEU GLN ASP GLN VAL PHE SER GLU PHE SEQRES 9 C 187 GLY PHE PRO PRO ALA VAL GLN ARG TRP VAL ILE GLY ARG SEQRES 10 C 187 CYS LEU CYS MET PRO GLU ARG SER LEU ALA SER TYR GLY SEQRES 11 C 187 VAL SER GLN ASP GLY ASP PRO ALA PHE LEU TYR LEU LEU SEQRES 12 C 187 SER ALA PRO ARG GLU VAL SER GLY GLN SER LEU GLN ASN SEQRES 13 C 187 SER LYS MET ASP ARG LYS LEU GLY LEU PHE PRO GLN SER SEQRES 14 C 187 LEU GLY LEU PRO HIS ASP LEU GLN PRO SER SER SER SER SEQRES 15 C 187 LEU PRO SER PRO SER HET GOL B 701 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 4 GOL C3 H8 O3 FORMUL 5 HOH *21(H2 O) HELIX 1 AA1 LYS A 4 GLY A 21 1 18 HELIX 2 AA2 ASP A 23 GLN A 37 1 15 HELIX 3 AA3 THR A 80 GLY A 93 1 14 HELIX 4 AA4 PRO A 95 SER A 97 5 3 HELIX 5 AA5 LEU A 114 GLY A 118 5 5 HELIX 6 AA6 ARG B 474 ALA B 495 1 22 HELIX 7 AA7 SER B 498 GLY B 510 1 13 HELIX 8 AA8 VAL B 513 ASP B 537 1 25 HELIX 9 AA9 PRO B 538 GLY B 541 5 4 HELIX 10 AB1 SER B 544 ARG B 555 1 12 HELIX 11 AB2 ASN B 558 LEU B 580 1 23 HELIX 12 AB3 GLY B 583 GLU B 586 5 4 HELIX 13 AB4 GLY B 587 HIS B 595 1 9 HELIX 14 AB5 ASP B 598 LEU B 618 1 21 HELIX 15 AB6 GLU C 170 GLY C 183 1 14 HELIX 16 AB7 ASP C 184 HIS C 198 1 15 HELIX 17 AB8 GLU C 208 PHE C 211 5 4 HELIX 18 AB9 SER C 246 GLY C 259 1 14 HELIX 19 AC1 PRO C 261 ALA C 263 5 3 HELIX 20 AC2 LEU C 280 GLY C 284 5 5 SHEET 1 AA1 2 LEU A 41 VAL A 45 0 SHEET 2 AA1 2 LEU C 202 LEU C 206 -1 O GLN C 205 N ARG A 42 SHEET 1 AA2 4 THR A 68 VAL A 75 0 SHEET 2 AA2 4 ILE A 55 ASP A 63 -1 N ILE A 55 O VAL A 75 SHEET 3 AA2 4 GLY A 125 LEU A 130 1 O LEU A 128 N SER A 60 SHEET 4 AA2 4 GLN A 99 VAL A 102 -1 N GLN A 100 O TYR A 129 SHEET 1 AA3 5 VAL C 237 ILE C 241 0 SHEET 2 AA3 5 ILE C 216 GLU C 223 -1 N LEU C 218 O LEU C 239 SHEET 3 AA3 5 PRO C 291 LEU C 296 1 O LEU C 296 N GLU C 223 SHEET 4 AA3 5 GLN C 265 ILE C 269 -1 N ARG C 266 O TYR C 295 SHEET 5 AA3 5 CYS C 272 LEU C 273 -1 O CYS C 272 N ILE C 269 CISPEP 1 GLY C 214 PRO C 215 0 -6.67 SITE 1 AC1 6 HIS B 615 GLN B 616 LEU B 618 TRP B 619 SITE 2 AC1 6 VAL C 222 HIS C 236 CRYST1 143.902 59.732 58.554 90.00 97.42 90.00 C 1 2 1 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.006949 0.000000 0.000905 0.00000 SCALE2 0.000000 0.016741 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017222 0.00000